ENST00000440090.5:n.82+266T>A

Variant names:

• chr6-134465324-T-A
• rs7743107
• ENST00000440090.5:n.82+266T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000440090.5(LINC01010):​n.82+266T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,224 control chromosomes in the GnomAD database, including 2,819 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (2819 hom., cov: 32)
• Consequence: LINC01010 ENST00000440090.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 2 publications found

Genes affected

LINC01010 (HGNC:48978): (long intergenic non-protein coding RNA 1010)

CT69 (HGNC:37196): (cancer/testis associated transcript 69)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01010	NR_038216.1	n.484+266T>A		intron_variant	Intron 2 of 2
LINC01010	NR_038217.1	n.275+475T>A		intron_variant	Intron 2 of 2
LINC01010	NR_038218.1	n.241+475T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01010	ENST00000440090.5	n.82+266T>A		intron_variant	Intron 1 of 2	1
LINC01010	ENST00000742854.1	n.772T>A		non_coding_transcript_exon_variant	Exon 2 of 2
CT69	ENST00000417483.5	n.187+9792A>T		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19022 AN: 152106 Hom.: 2810 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.00302

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.116

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.125 AC: 19063 AN: 152224 Hom.: 2819 Cov.: 32 AF XY: 0.123 AC XY: 9172 AN XY: 74436

African (AFR) AF: 0.359 AC: 14895 AN: 41496

American (AMR) AF: 0.0595 AC: 911 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0640 AC: 222 AN: 3468

East Asian (EAS) AF: 0.154 AC: 799 AN: 5178

South Asian (SAS) AF: 0.101 AC: 487 AN: 4822

European-Finnish (FIN) AF: 0.00302 AC: 32 AN: 10612

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0213 AC: 1450 AN: 68024

Other (OTH) AF: 0.116 AC: 246 AN: 2112

Alfa AF: 0.0808 Hom.: 196

Bravo AF: 0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.6
DANN	Benign	0.70
PhyloP100		0.096

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7743107; hg19: chr6-134786462;